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Preheat oven to 350F degrees.
Place shallots, scallions, garlic, and thyme or rosemary in a small baking dish and cover with olive oil. Cook for about 40 minutes, until golden brown and completely soft when pierced with a knife or toothpick. Let onions cool completely in the olive oil. Reserve 2 tablespoons infused olive oil for garnish (you can store the remainder in an airtight container in the refrigerator for marinades, dressings, or roasting vegetables!).
Transfer cooled onions to a paper towel to blot away excess oil, then finely chop with a sharp knife. Stir all but 2 tablespoons chopped onions into labne with a pinch of flaky sea salt in a medium serving bowl and stir until well combined. Top with reserved chopped onions and olive oil, then sprinkle with sliced scallions. Finish with a sprinkle of flaky sea salt and refrigerate until ready to serve.
Serve confit onion labne dip with toasted pita or crackers and fresh vegetables for dipping.